Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001092.1 Corchorus capsularis cultivar CVL-1 contig01092, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 626

Length: 1044
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28


Found at i:409 original size:8 final size:7

Alignment explanation


    Indices: 398--448  Score: 52
    Period size: 7  Copynumber: 7.4  Consensus size: 7

        388 CAAAATTAAC

                   
        398 AAAAACA
          1 AAAAACA

                    
        405 CAAAAACA
          1 -AAAAACA

                   
        413 AAAAAC-
          1 AAAAACA

                   
        419 AAAAACA
          1 AAAAACA

               *  *
        426 AAATACG
          1 AAAAACA

                  *
        433 AAAAA-T
          1 AAAAACA

                   
        439 AAAAACA
          1 AAAAACA

               
        446 AAA
          1 AAA

        449 CTAAAGGAAA


Statistics
Matches: 36,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
   6   11  0.31
   7   18  0.50
   8    7  0.19

ACGTcount: A:0.80, C:0.14, G:0.02, T:0.04


Consensus pattern (7 bp):   
AAAAACA

Found at i:420 original size:13 final size:13

Alignment explanation


    Indices: 395--448  Score: 65
    Period size: 13  Copynumber: 4.1  Consensus size: 13

        385 CTGCAAAATT

                          
        395 AACAAAAACACAAA
          1 AACAAAAA-ACAAA

                         
        409 AACAAAAAACAAA
          1 AACAAAAAACAAA

                   *      
        422 AACAAAATACGAAA
          1 AACAAAAAAC-AAA

               *         
        436 AA-TAAAAACAAA
          1 AACAAAAAACAAA

             
        448 A
          1 A

        449 CTAAAGGAAA


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  12    4  0.11
  13   19  0.53
  14   13  0.36

ACGTcount: A:0.80, C:0.15, G:0.02, T:0.04


Consensus pattern (13 bp):   
AACAAAAAACAAA

Found at i:422 original size:5 final size:6

Alignment explanation


    Indices: 399--448  Score: 55
    Period size: 6  Copynumber: 7.7  Consensus size: 6

        389 AAAATTAACA

                                                        *            
        399 AAAACAC AAAAAC AAAAAAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
          1 AAAA-AC AAAAAC -AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA

        449 CTAAAGGAAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
   6   21  0.55
   7   13  0.34
   8    4  0.11

ACGTcount: A:0.80, C:0.14, G:0.02, T:0.04


Consensus pattern (6 bp):   
AAAAAC

Found at i:436 original size:20 final size:20

Alignment explanation


    Indices: 395--448  Score: 72
    Period size: 20  Copynumber: 2.6  Consensus size: 20

        385 CTGCAAAATT

                                 
        395 AACAAAAACACAAAAACAAAA
          1 AACAAAAACA-AAAAACAAAA

                         *  *   
        416 AACAAAAACAAAATACGAAA
          1 AACAAAAACAAAAAACAAAA

              *          
        436 AATAAAAACAAAA
          1 AACAAAAACAAAA

        449 CTAAAGGAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  20   20  0.67
  21   10  0.33

ACGTcount: A:0.80, C:0.15, G:0.02, T:0.04


Consensus pattern (20 bp):   
AACAAAAACAAAAAACAAAA
Done.